The interaction of sub-micron scale objects with fluids is an important problem encountered in miniaturized systems. Various physical phenomena should be modeled simultaneously for a fundamental investigation of these systems. Our objective is to develop a direct numerical simulation tool to better understand the motion of sub-micron objects in complex geometries. We report: (a) A novel methodology to simulate the Brownian motion of objects in fluids, (b) A technique to simulate the motion of electrically charged bodies with thin Debye layers & (c) An innovative approach to simulate the motion of flexible bodies. The goal is to develop numerical techniques for each of these problems such that they can be unified or interfaced to allow simultaneous description of complex physical phenomena. Preliminary work has been accomplished.